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<A HREF="#_A_">A</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_P_">P</A> <A HREF="#_Q_">Q</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <HR>
<A NAME="_A_"><!-- --></A><H2>
<B>A</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/stuff/AA_Mapper.html" title="class in de.hu.berlin.wbi.stuff"><B>AA_Mapper</B></A> - Class in <A HREF="./de/hu/berlin/wbi/stuff/package-summary.html">de.hu.berlin.wbi.stuff</A><DD>A base class for extracting Mutations from text<DT><A HREF="./de/hu/berlin/wbi/stuff/AA_Mapper.html#AA_Mapper()"><B>AA_Mapper()</B></A> - 
Constructor for class de.hu.berlin.wbi.stuff.<A HREF="./de/hu/berlin/wbi/stuff/AA_Mapper.html" title="class in de.hu.berlin.wbi.stuff">AA_Mapper</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html#addHgvs(java.lang.String)"><B>addHgvs(String)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml">SNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#addMutation(java.lang.String)"><B>addMutation(String)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#addMutations(java.util.Set)"><B>addMutations(Set&lt;String&gt;)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html#addPSM(de.hu.berlin.wbi.stuff.xml.PSM)"><B>addPSM(PSM)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml">SNP</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_C_"><!-- --></A><H2>
<B>C</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html#characters(char[], int, int)"><B>characters(char[], int, int)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html" title="class in de.hu.berlin.wbi.stuff.xml">ParseXML</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/osiris/CheckOsiris.html" title="class in de.hu.berlin.wbi.process.osiris"><B>CheckOsiris</B></A> - Class in <A HREF="./de/hu/berlin/wbi/process/osiris/package-summary.html">de.hu.berlin.wbi.process.osiris</A><DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/process/osiris/CheckOsiris.html#CheckOsiris()"><B>CheckOsiris()</B></A> - 
Constructor for class de.hu.berlin.wbi.process.osiris.<A HREF="./de/hu/berlin/wbi/process/osiris/CheckOsiris.html" title="class in de.hu.berlin.wbi.process.osiris">CheckOsiris</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#cleanResults(java.util.List)"><B>cleanResults(List&lt;dbSNPNormalized&gt;)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Sometimes one SNP mention can be normalized to the same dbSNP identifier 
 several times.
<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#closeQuery()"><B>closeQuery()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>Close resultset
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#compareTo(de.hu.berlin.wbi.objects.dbSNPNormalized)"><B>compareTo(dbSNPNormalized)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#connect()"><B>connect()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>Connects with database
</DL>
<HR>
<A NAME="_D_"><!-- --></A><H2>
<B>D</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects"><B>DatabaseConnection</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Convenience class for database communication<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#DatabaseConnection(java.util.Properties)"><B>DatabaseConnection(Properties)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>Set up a database connection, by using a java-property object
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><B>dbSNP</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Represents a <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/">dbSNP</a>
 entry; loaded from a local database.<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#dbSNP()"><B>dbSNP()</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>Simple constructor
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#dbSNP(int, int, java.util.Set, int, java.lang.String)"><B>dbSNP(int, int, Set&lt;String&gt;, int, String)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects"><B>dbSNPNormalized</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Represents a <CODE>Mutation</CODE> mention which has been successfully
 normalized to a <A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> .<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#dbSNPNormalized(de.hu.berlin.wbi.objects.dbSNP, boolean, boolean, boolean, de.hu.berlin.wbi.objects.UniprotFeature, boolean)"><B>dbSNPNormalized(dbSNP, boolean, boolean, boolean, UniprotFeature, boolean)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/package-summary.html"><B>de.hu.berlin.wbi.objects</B></A> - package de.hu.berlin.wbi.objects<DD>Package with the main data objects.<DT><A HREF="./de/hu/berlin/wbi/process/package-summary.html"><B>de.hu.berlin.wbi.process</B></A> - package de.hu.berlin.wbi.process<DD>Various common work-flows based on SNP normalization.<DT><A HREF="./de/hu/berlin/wbi/process/osiris/package-summary.html"><B>de.hu.berlin.wbi.process.osiris</B></A> - package de.hu.berlin.wbi.process.osiris<DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/psb/package-summary.html"><B>de.hu.berlin.wbi.psb</B></A> - package de.hu.berlin.wbi.psb<DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/stuff/package-summary.html"><B>de.hu.berlin.wbi.stuff</B></A> - package de.hu.berlin.wbi.stuff<DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/package-summary.html"><B>de.hu.berlin.wbi.stuff.xml</B></A> - package de.hu.berlin.wbi.stuff.xml<DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#disconnect()"><B>disconnect()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>Disconnects from database
</DL>
<HR>
<A NAME="_E_"><!-- --></A><H2>
<B>E</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html#endElement(java.lang.String, java.lang.String, java.lang.String)"><B>endElement(String, String, String)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html" title="class in de.hu.berlin.wbi.stuff.xml">ParseXML</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects"><B>EntityOffset</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Represents the text span of entity mentions (<CODE>Mutation</CODE>, <A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects"><CODE>Gene</CODE></A>, etc.).<DT><A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html#EntityOffset(int, int)"><B>EntityOffset(int, int)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>
<DD>Constructor with start and end offset
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/process/Evaluate.html" title="class in de.hu.berlin.wbi.process"><B>Evaluate</B></A> - Class in <A HREF="./de/hu/berlin/wbi/process/package-summary.html">de.hu.berlin.wbi.process</A><DD>Class is used to evaluate snp-normalizer; 
 Corpus is not provided due to licence restrictions but a link is provided in the paper..<DT><A HREF="./de/hu/berlin/wbi/process/Evaluate.html#Evaluate()"><B>Evaluate()</B></A> - 
Constructor for class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/Evaluate.html" title="class in de.hu.berlin.wbi.process">Evaluate</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/osiris/EvaluateOsiris.html" title="class in de.hu.berlin.wbi.process.osiris"><B>EvaluateOsiris</B></A> - Class in <A HREF="./de/hu/berlin/wbi/process/osiris/package-summary.html">de.hu.berlin.wbi.process.osiris</A><DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/process/osiris/EvaluateOsiris.html#EvaluateOsiris()"><B>EvaluateOsiris()</B></A> - 
Constructor for class de.hu.berlin.wbi.process.osiris.<A HREF="./de/hu/berlin/wbi/process/osiris/EvaluateOsiris.html" title="class in de.hu.berlin.wbi.process.osiris">EvaluateOsiris</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#executeUpdate(java.lang.String)"><B>executeUpdate(String)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>Wrapper for SQL execute update
</DL>
<HR>
<A NAME="_G_"><!-- --></A><H2>
<B>G</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects"><B>Gene</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Represents a gene mention found by any Named Enttiy Recognition and Normalization tool.<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#Gene()"><B>Gene()</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Empty constructor
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#Gene(int, int, int, int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)"><B>Gene(int, int, int, int, EntityOffset, String)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/psb/GenePSB.html" title="class in de.hu.berlin.wbi.psb"><B>GenePSB</B></A> - Class in <A HREF="./de/hu/berlin/wbi/psb/package-summary.html">de.hu.berlin.wbi.psb</A><DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/psb/GenePSB.html#GenePSB(java.lang.String)"><B>GenePSB(String)</B></A> - 
Constructor for class de.hu.berlin.wbi.psb.<A HREF="./de/hu/berlin/wbi/psb/GenePSB.html" title="class in de.hu.berlin.wbi.psb">GenePSB</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#getAaLoc()"><B>getAaLoc()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#getAaPosition()"><B>getAaPosition()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#getConfidence()"><B>getConfidence()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#getConfidence()"><B>getConfidence()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Gets the confidence for this gene.
<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#getConn()"><B>getConn()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html#getDbSNP()"><B>getDbSNP()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A>
<DD>Gets the associated dbSNP entry.
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#getEndLoc()"><B>getEndLoc()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>Returns end location of the modification on the peptide
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#getEntity()"><B>getEntity()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Gets the string in the text.
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html#getEntity()"><B>getEntity()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A>
<DD>Gets the actual entity mention
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#getEntrez()"><B>getEntrez()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#getFeatures(int)"><B>getFeatures(int)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>Returns all UniProt features for one specific Entrez-Gene Identifier
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#getGeneID()"><B>getGeneID()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#getGeneID()"><B>getGeneID()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Gets the gene-ID (Entrez in our case).
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#getGeneId()"><B>getGeneId()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>Returns associated Enzrez Gene ID
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#getHgvs()"><B>getHgvs()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html#getHgvs()"><B>getHgvs()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml">SNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#getLocation()"><B>getLocation()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Gets the found at which position.
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#getLocation()"><B>getLocation()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>Gets the location.
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#getLocation()"><B>getLocation()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Gets the location of the mutation
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#getModificationType()"><B>getModificationType()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>Returns modification type (e.g. signaling peptide)
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#getMutation()"><B>getMutation()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>Gets the mutation.
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#getMutations()"><B>getMutations()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#getMutResidue()"><B>getMutResidue()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Gets the residues.
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#getPmid()"><B>getPmid()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Gets the article ID.
<DT><A HREF="./de/hu/berlin/wbi/psb/MutationPSB.html#getPmid()"><B>getPmid()</B></A> - 
Method in class de.hu.berlin.wbi.psb.<A HREF="./de/hu/berlin/wbi/psb/MutationPSB.html" title="class in de.hu.berlin.wbi.psb">MutationPSB</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#getPosition()"><B>getPosition()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Gets the position.
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#getPossibledbSNPs(java.util.List, java.util.List)"><B>getPossibledbSNPs(List&lt;dbSNP&gt;, List&lt;UniprotFeature&gt;)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>This method evaluates if some of the <A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> provided in <b>candidates</b>
 actually equals the text-mined <CODE>Mutation</CODE>
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html#getPsms()"><B>getPsms()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml">SNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#getResidues()"><B>getResidues()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#getRs()"><B>getRs()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#getRsID()"><B>getRsID()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html#getRsId()"><B>getRsId()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml">SNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#getSNP(int)"><B>getSNP(int)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>Retrieves a list of dbSNP entries associated with a specific entrez-gene ID
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#getSpecies()"><B>getSpecies()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Gets the species.
<DT><A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html#getStart()"><B>getStart()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>
<DD>Get start character
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#getStartLoc()"><B>getStartLoc()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>Returns start location of the modification on the peptide
<DT><A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html#getStop()"><B>getStop()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>
<DD>Get end character position
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#getType()"><B>getType()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>Gets the mutation type (e.g. c., p.,  or g.)
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html#getType()"><B>getType()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A>
<DD>Gets the either NSM or PSM.
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#getWildtype()"><B>getWildtype()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#getWildtype()"><B>getWildtype()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>Gets the wild-type.
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#getWildtype()"><B>getWildtype()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#getWtResidue()"><B>getWtResidue()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Gets the residue.
</DL>
<HR>
<A NAME="_H_"><!-- --></A><H2>
<B>H</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#hashCode()"><B>hashCode()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html#hashCode()"><B>hashCode()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#hashCode()"><B>hashCode()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#hashCode()"><B>hashCode()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects"><B>HGVS</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Represents a <a href="http://www.hgvs.org/">HGVS</a> reference, like <tt>NR_027062.1:c.157+25766C>T</tt>.<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#HGVS(java.lang.String)"><B>HGVS(String)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_I_"><!-- --></A><H2>
<B>I</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#init(de.hu.berlin.wbi.objects.DatabaseConnection, java.lang.String, java.lang.String)"><B>init(DatabaseConnection, String, String)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>Initializes the prepared statements
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#init(de.hu.berlin.wbi.objects.DatabaseConnection, java.lang.String, java.lang.String)"><B>init(DatabaseConnection, String, String)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Initializes the prepared statements
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#init(de.hu.berlin.wbi.objects.DatabaseConnection, java.lang.String)"><B>init(DatabaseConnection, String)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>Initializes prepared statements to retrieve UniProt features
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#isAlleleOrder()"><B>isAlleleOrder()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>Returns true if Alleles are in the same order in dbSNP as in the text mention
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#isExactMatch()"><B>isExactMatch()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#isFeatureMatch()"><B>isFeatureMatch()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#isMethioneMatch()"><B>isMethioneMatch()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#isNsm()"><B>isNsm()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Checks if is flag indicating if this SNP is possibly a NSM.
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#isPsm()"><B>isPsm()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#isValid()"><B>isValid()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>Checks if the PSM object is valid.
</DL>
<HR>
<A NAME="_M_"><!-- --></A><H2>
<B>M</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/process/Evaluate.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/Evaluate.html" title="class in de.hu.berlin.wbi.process">Evaluate</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/MinimalExample.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/MinimalExample.html" title="class in de.hu.berlin.wbi.process">MinimalExample</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/ModifyOsiris.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/ModifyOsiris.html" title="class in de.hu.berlin.wbi.process">ModifyOsiris</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/Normalize.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/Normalize.html" title="class in de.hu.berlin.wbi.process">Normalize</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/NormalizeDB.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/NormalizeDB.html" title="class in de.hu.berlin.wbi.process">NormalizeDB</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/osiris/CheckOsiris.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.process.osiris.<A HREF="./de/hu/berlin/wbi/process/osiris/CheckOsiris.html" title="class in de.hu.berlin.wbi.process.osiris">CheckOsiris</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/osiris/EvaluateOsiris.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.process.osiris.<A HREF="./de/hu/berlin/wbi/process/osiris/EvaluateOsiris.html" title="class in de.hu.berlin.wbi.process.osiris">EvaluateOsiris</A>
<DD>Evaluate our normalization procedure on the Osiris corpus.
<DT><A HREF="./de/hu/berlin/wbi/psb/Normalize.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.psb.<A HREF="./de/hu/berlin/wbi/psb/Normalize.html" title="class in de.hu.berlin.wbi.psb">Normalize</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html" title="class in de.hu.berlin.wbi.stuff.xml">ParseXML</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/MinimalExample.html" title="class in de.hu.berlin.wbi.process"><B>MinimalExample</B></A> - Class in <A HREF="./de/hu/berlin/wbi/process/package-summary.html">de.hu.berlin.wbi.process</A><DD>Class contains source code for a minimal example, required to normalize a SNP<DT><A HREF="./de/hu/berlin/wbi/process/MinimalExample.html#MinimalExample()"><B>MinimalExample()</B></A> - 
Constructor for class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/MinimalExample.html" title="class in de.hu.berlin.wbi.process">MinimalExample</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/ModifyOsiris.html" title="class in de.hu.berlin.wbi.process"><B>ModifyOsiris</B></A> - Class in <A HREF="./de/hu/berlin/wbi/process/package-summary.html">de.hu.berlin.wbi.process</A><DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/process/ModifyOsiris.html#ModifyOsiris()"><B>ModifyOsiris()</B></A> - 
Constructor for class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/ModifyOsiris.html" title="class in de.hu.berlin.wbi.process">ModifyOsiris</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects"><B>MutationMention</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Class to represent a mutation mention found by an NER tool like 
 MutationFinder or SETH<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#MutationMention()"><B>MutationMention()</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#MutationMention(java.lang.String)"><B>MutationMention(String)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Generates a Mutation object from a String like "A123T".
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#MutationMention(de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)"><B>MutationMention(EntityOffset, String)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/psb/MutationPSB.html" title="class in de.hu.berlin.wbi.psb"><B>MutationPSB</B></A> - Class in <A HREF="./de/hu/berlin/wbi/psb/package-summary.html">de.hu.berlin.wbi.psb</A><DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/psb/MutationPSB.html#MutationPSB(java.lang.String)"><B>MutationPSB(String)</B></A> - 
Constructor for class de.hu.berlin.wbi.psb.<A HREF="./de/hu/berlin/wbi/psb/MutationPSB.html" title="class in de.hu.berlin.wbi.psb">MutationPSB</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects"><B>MutationValidation</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>This object represents a <CODE>Mutation</CODE> from the validation corpus, where
 we already know which <A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> entry is associated with this gene.<DT><A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html#MutationValidation(int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String)"><B>MutationValidation(int, EntityOffset, String, String, String, String, String)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A>
<DD>Constructor
</DL>
<HR>
<A NAME="_N_"><!-- --></A><H2>
<B>N</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/process/Normalize.html" title="class in de.hu.berlin.wbi.process"><B>Normalize</B></A> - Class in <A HREF="./de/hu/berlin/wbi/process/package-summary.html">de.hu.berlin.wbi.process</A><DD>This is an example class for using snp-normalizer<DT><A HREF="./de/hu/berlin/wbi/process/Normalize.html#Normalize()"><B>Normalize()</B></A> - 
Constructor for class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/Normalize.html" title="class in de.hu.berlin.wbi.process">Normalize</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/psb/Normalize.html" title="class in de.hu.berlin.wbi.psb"><B>Normalize</B></A> - Class in <A HREF="./de/hu/berlin/wbi/psb/package-summary.html">de.hu.berlin.wbi.psb</A><DD>&nbsp;<DT><A HREF="./de/hu/berlin/wbi/psb/Normalize.html#Normalize()"><B>Normalize()</B></A> - 
Constructor for class de.hu.berlin.wbi.psb.<A HREF="./de/hu/berlin/wbi/psb/Normalize.html" title="class in de.hu.berlin.wbi.psb">Normalize</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/process/NormalizeDB.html" title="class in de.hu.berlin.wbi.process"><B>NormalizeDB</B></A> - Class in <A HREF="./de/hu/berlin/wbi/process/package-summary.html">de.hu.berlin.wbi.process</A><DD>Class is used to normalize all mutation mentions stored in a database to SNPs<DT><A HREF="./de/hu/berlin/wbi/process/NormalizeDB.html#NormalizeDB()"><B>NormalizeDB()</B></A> - 
Constructor for class de.hu.berlin.wbi.process.<A HREF="./de/hu/berlin/wbi/process/NormalizeDB.html" title="class in de.hu.berlin.wbi.process">NormalizeDB</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_P_"><!-- --></A><H2>
<B>P</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html" title="class in de.hu.berlin.wbi.stuff.xml"><B>ParseXML</B></A> - Class in <A HREF="./de/hu/berlin/wbi/stuff/xml/package-summary.html">de.hu.berlin.wbi.stuff.xml</A><DD>Class is used to parse dbSNP XML<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html#ParseXML()"><B>ParseXML()</B></A> - 
Constructor for class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html" title="class in de.hu.berlin.wbi.stuff.xml">ParseXML</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/AA_Mapper.html#populateAminoAcidThreeToOneLookupMap()"><B>populateAminoAcidThreeToOneLookupMap()</B></A> - 
Static method in class de.hu.berlin.wbi.stuff.<A HREF="./de/hu/berlin/wbi/stuff/AA_Mapper.html" title="class in de.hu.berlin.wbi.stuff">AA_Mapper</A>
<DD>This method simple fills the two mappings between amino acid one letter code and the amino acid three letter code
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml"><B>PSM</B></A> - Class in <A HREF="./de/hu/berlin/wbi/stuff/xml/package-summary.html">de.hu.berlin.wbi.stuff.xml</A><DD>Class represents a protein sequence mutation<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#PSM(int, int, java.lang.String, java.lang.String)"><B>PSM(int, int, String, String)</B></A> - 
Constructor for class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_Q_"><!-- --></A><H2>
<B>Q</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html#query(java.lang.String)"><B>query(String)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>
<DD>Wrapper for querying the database
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#queryGenesForArticle(int)"><B>queryGenesForArticle(int)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>Search for all genes contained in an Article using PubMed ID.
</DL>
<HR>
<A NAME="_R_"><!-- --></A><H2>
<B>R</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#readMutations(java.lang.String)"><B>readMutations(String)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>This method loads Mutations from a file which are in the following format
 described in data/snps.txt (PMID\tWMutM\tstart\tstop)
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html#readMutationsValidation(java.lang.String)"><B>readMutationsValidation(String)</B></A> - 
Static method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A>
<DD>Reads the mutation from the annotated corpus and returns these mutations.
</DL>
<HR>
<A NAME="_S_"><!-- --></A><H2>
<B>S</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#setAaLoc(int)"><B>setAaLoc(int)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#setAaPosition(int)"><B>setAaPosition(int)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#setEntrez(int)"><B>setEntrez(int)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#setGeneID(int)"><B>setGeneID(int)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#setHgvs(java.util.Set)"><B>setHgvs(Set&lt;HGVS&gt;)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#setLocation(de.hu.berlin.wbi.objects.EntityOffset)"><B>setLocation(EntityOffset)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Sets the position of the mutation
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#setMutResidue(java.lang.String)"><B>setMutResidue(String)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Sets the residues.
<DT><A HREF="./de/hu/berlin/wbi/psb/GenePSB.html#setPmid(int)"><B>setPmid(int)</B></A> - 
Method in class de.hu.berlin.wbi.psb.<A HREF="./de/hu/berlin/wbi/psb/GenePSB.html" title="class in de.hu.berlin.wbi.psb">GenePSB</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/psb/MutationPSB.html#setPmid(int)"><B>setPmid(int)</B></A> - 
Method in class de.hu.berlin.wbi.psb.<A HREF="./de/hu/berlin/wbi/psb/MutationPSB.html" title="class in de.hu.berlin.wbi.psb">MutationPSB</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#setPosition(java.lang.String)"><B>setPosition(String)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Sets the position.
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#setResidues(java.util.Set)"><B>setResidues(Set&lt;String&gt;)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#setRsID(int)"><B>setRsID(int)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#setWildtype(java.lang.String)"><B>setWildtype(String)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#setWtResidue(java.lang.String)"><B>setWtResidue(String)</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>Sets the residue.
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml"><B>SNP</B></A> - Class in <A HREF="./de/hu/berlin/wbi/stuff/xml/package-summary.html">de.hu.berlin.wbi.stuff.xml</A><DD>Represents a SNP 
  consisting of dbSNP id
  several (at least one) protein sequence mutations
  several HGVS representations<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html#SNP(int)"><B>SNP(int)</B></A> - 
Constructor for class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml">SNP</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)"><B>startElement(String, String, String, Attributes)</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/ParseXML.html" title="class in de.hu.berlin.wbi.stuff.xml">ParseXML</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_T_"><!-- --></A><H2>
<B>T</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#toNormalized()"><B>toNormalized()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNP.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/Gene.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/HGVS.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationMention.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>(non-Javadoc)
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/PSM.html" title="class in de.hu.berlin.wbi.stuff.xml">PSM</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.berlin.wbi.stuff.xml.<A HREF="./de/hu/berlin/wbi/stuff/xml/SNP.html" title="class in de.hu.berlin.wbi.stuff.xml">SNP</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_U_"><!-- --></A><H2>
<B>U</B></H2>
<DL>
<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects"><B>UniprotFeature</B></A> - Class in <A HREF="./de/hu/berlin/wbi/objects/package-summary.html">de.hu.berlin.wbi.objects</A><DD>Represents a <a href="./de/hu/berlin/wbi/objects/www.uniprot.org/">UniProt</a>
 entry; loaded from database.<DT><A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html#UniprotFeature(int, java.lang.String, int, int)"><B>UniprotFeature(int, String, int, int)</B></A> - 
Constructor for class de.hu.berlin.wbi.objects.<A HREF="./de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>
<DD>&nbsp;
</DL>
<HR>
<A HREF="#_A_">A</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_P_">P</A> <A HREF="#_Q_">Q</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> 

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